Integration and Clustering

Uncorrected UMAP

scVI corrected UMAP

Annotation

Old annotation

Kruskal-Wallis Test

TCR

Present clones arranged from largest to smallest.

Number of clones (not cells!) per type and sample

Percentage of T cells that have a TCR (TRUE) and don’t have one (FALSE).

Note that here we are including NKs in the T cell compartment, which are not expected to have TCRs.

## 
## FALSE  TRUE 
##  9460 40187
## 
## FALSE  TRUE 
## 19.05 80.95

Clone size by cell type & disease

Top 10 clones by sample

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